The Warlords wouldn't be very well represented as colonies- in fact, I honestly feel like Semper Fi era- HoI3 was probably their best representation. For starters, it wouldn't make sense for Japan's gameplay- When they came into China, they didn't just replace Yan Xishan and call it a day- they smashed it into one part puppet state (via Mengjiang) which was supposed to be an Inner Mongolian government, and one part direct occupation area. The outer cliques I could see more, but I think the whole annexation-occupation concept works pretty well for them- after all, if Japan was able to capture, say, Ma Hongkui (represented in game as occupying Xibei San Ma's capital), I'd imagine that'd be the trigger for collapse of the entire Ma Clique army- after all, people are serving them instead of Kai-Shek for a reason. Then it'd just be yet another front Chiang now has to stretch his forces to.
On that subject, I don't think Japan's starting territory would be very well as colonies. Korea was treated as a direct part of Japan (no occupation or colony or anything) after the southern expansion plan started coming to fruition- maybe it spends a few years as a colony until being annexed fully when Marco Polo Bridge happens?- and Manchukuo was a proper enough government that I think it itself would be better as a proper puppet than a colony- I'd compare its level of independence more to the likes of Slovakia than I would the Raj, just more of a Japanese military presence there for those rebels and the like. Mengiang and China-Nanjing, however, I think would definitely work as your definition of colonies (which I think is a pretty good idea, myself).
The real question comes down to colonial size and scope. It's easy to point to, say, the Raj, and say "That's a colony". But what of British Africa? After all, by this point, there's an unbroken line from Sudan to Botswana (I think I'd agree with Darkest Hour's definition that Egypt would be better represented as a Puppet State than colony), as well as from Morocco to the modern RoC. If we draw them at every country, British Africa would be an outright nightmare, especially given modern nations that are the size of one traditional HoI province, and they wouldn't even be particularly useful for the UK. On the other hand, having a massive "British Africa" wouldn't be quite a good representation either. Sudan'd be the trickiest case, I think, since Britain and Egypt technically shared ownership.
So, what were you thinking on that, then?
